A DFTB study on the electronic response of encapsulated DNA nucleobases onto chiral CNTs as a sequencer

Sequencing the DNA nucleobases is essential in the diagnosis and treatment of many diseases related to human genes. In this article, the encapsulation of DNA nucleobases with some of the important synthesized chiral (7, 6), (8, 6), and (10, 8) carbon nanotubes were investigated. The structures were modeled by applying density functional theory based on tight binding method (DFTB) by considering semi-empirical basis sets. Encapsulating DNA nucleobases on the inside of CNTs caused changes in the electronic properties of the selected chiral CNTs. The results confirmed that van der Waals (vdW) interactions, π-orbitals interactions, non-bonded electron pairs, and the presence of high electronegative atoms are the key factors for these changes. The result of electronic parameters showed that among the CNTs, CNT (8, 6) is a suitable choice in sequencing guanine (G) and cytosine (C) DNA nucleobases. However, they are not able to sequence adenine (A) and thymine (T). According to the band gap energy engineering approach and absorption energy, the presence of G and C DNA nucleobases decreased the band gap energy of CNTs. Hence selected CNTs suggested as biosensor substrates for sequencing G and C DNA nucleobases.

Computational assessment of thermostability in miRNA:CNT system using molecular dynamics simulations

BACKGROUND

Carbon nanotubes (CNTs) show great promise as theranostic agents due to their drug delivery properties, intrinsic near-infrared radiation-responsiveness, and magnetic functionalization. However, temperature elevation caused by these external stimuli during drug delivery should be considered for the evaluation of CNT-based systems loaded with temperature-sensitive biomolecules.

METHODS

We examine the thermal stability of a 33 nucleotides long hairpin miRNA encapsulated in (20,20) CNT using all-atom molecular dynamics simulations in explicit water. We systematically increase the temperature as 298, 310, 327, and 343 K, reaching the melting temperature of miRNA. To emphasize the effect of the aromatic confined space, we compare the dynamics of miRNA inside the CNT to its dynamics free in the solution at the same temperatures, reaching a total simulation time of 7.9 μs.

RESULTS

miRNA hairpin mostly maintains its double-stranded structure in the confined CNT, even at elevated temperatures. Binding free energies and potential of mean force calculations also underline the strong π-π interactions between the biomolecule and the CNT for 298-343 K.

CONCLUSION

The let-7 miRNA mimic, which represents a wide family of RNAi-based therapeutics, can be transported in the CNT under medically applied hyperthermic conditions.

GENERAL SIGNIFICANCE

This study shows how the structure and dynamics of miRNA hairpin are affected when encapsulated in an aromatic tube, during a systematic increase of temperature. It also indicates the high potential of CNT-based systems for the delivery of oligonucleotide therapeutics while simultaneous imaging/magnetic field guiding to the target tissue is achieved.

Interaction Mechanism of Doxorubicin and SWCNT: Protonation and Diameter Effects on the Drug Loading and Releasing

In the present work the adsorption of doxorubicin (DOX) on the surface of single-walled carbon nanotube (SWCNT) as well as its encapsulation in SWCNT, and their dependence on the protonation of NH2 group of DOX, solvent, and the diameter of armchair (n,n) SWCNT were systematically investigated using theoretical methods such as PM6-DH2 and M06-2X in the scheme of OMIOM. It was found that the two loadings, adsorption on the sidewall of CNT and the encapsulation in CNT, have distinct solvent, protonation and diameter dependences. The encapsulation is much stronger than the adsorption of DOX on the sidewall of CNT, and the former also has significantly higher solvent and protonation effects than the latter. The adsorption primarily occurs through π-π stacking and just becomes slightly stronger as the diameter of CNT increases, while besides π-π stacking the additional C-H/N-H/O-H…π and C=O…π also contribute to the encapsulation of DOX in CNT. It seems that (8,8) CNT (diameter ~ 11Å) energetically is an onset for the encapsulation since the encapsulation turns from endothermic to exothermic as the diameter is larger than approximately 11 Å, and the optimal diameter for the encapsulation is 14Å corresponding to (10,10) CNT. Thus for the thick CNT the encapsulation may also play an important role in the loading and releasing for the CNT-based drug delivery system of the DOX.

Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form

Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter of debate. Using enhanced sampling techniques, we show for the first time that, given a sufficiently large carbon nanotube, the confinement of a double-stranded DNA segment, 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', is thermodynamically favourable under physiological environments (134 mM, 310 K, 1 bar), leading to DNA-nanotube hybrids with lower free energy than the unconfined biomolecule. A diameter threshold of 3 nm is established below which encapsulation is inhibited. The confined DNA segment maintains its translational mobility and exhibits the main geometrical features of the canonical B form. To accommodate itself within the nanopore, the DNA's end-to-end length increases from 3.85 nm up to approximately 4.1 nm, due to a ~0.3 nm elastic expansion of the strand termini. The canonical Watson-Crick H-bond network is essentially conserved throughout encapsulation, showing that the contact between the DNA segment and the hydrophobic carbon walls results in minor rearrangements of the nucleotides H-bonding. The results obtained here are paramount to the usage of carbon nanotubes as encapsulation media for next generation drug delivery technologies.

Noncovalent interaction of carbon nanostructures

The potential application of carbon nanomaterials in biology and medicine increases the necessity to understand the nature of their interactions with living organisms and the environment. The primary forces of interaction at the nano-bio interface are mostly noncovalent in nature. Quantifying such interactions and identifying various factors that influence such interactions is a question of outstanding fundamental interest in academia and industry. In this Account, we have summarized our recent studies in understanding the noncovalent interactions of carbon nanostructures (CNSs), which were obtained by employing first-principles calculations on various model systems representing carbon nanotubes (CNTs) and graphene. Bestowed with an extended sp(2) carbon network, which is a common feature in all of these nanostructures, they exhibit π-π interactions with aromatic molecules (benzene, naphthalene, nucleobases, amino acids), cation-π type of interactions with metal ions, anion-π interactions with anions, and other XH···π type of interactions with various small molecules (H2O, NH3, CH4, H2, etc.). CNTs are wrapped-up forms of two-dimensional graphene, and hence, it is interesting to compare the binding abilities of these two allotropes that differ in their curvature. The chirality and curvature of CNSs appear to play a major role in determining the structural, energetic, and functional properties. Flat graphene shows stronger noncovalent interactions than the curved nanotubes toward various substrates. Understanding the interactions of CNSs with organic molecules and biomolecules has gained a great deal of research interest because of their potential applications in various fields. Aromatic hydrocarbons show a strong propensity to interact with CNSs via the π-π mode of interaction rather than CH···π interaction. As DNA sequencing appears to be one of the most important potential applications of carbon nanomaterials, the study of CNS-nucleobase interactions has become quite important. The nucleobases are physisorbed on the surface of CNSs in the order G > T ≈ A > C > U, exhibiting π-π-stacking type of interaction. These interactions become stronger as the curvature of the CNSs decreases. It is also indispensable to study the interaction of nanomaterials with proteins and especially with amino acids at a molecular level to understand the drug delivery mechanism of CNSs. We have shown that the CNSs interact with small molecules by means of physisorption and thus show potential for sensor applications. The prime requisite for the exploitation of these CNSs in nanoelectronics is the tunable energy gap. We have revealed that metal ion doping modulates the HOMO-LUMO energy gap of the nanotubes significantly and thus provides a handle to tune the electronic and conductivity properties of CNTs. Moreover, metal ions tend to selectively bind with nanotubes of different chirality such as armchair and zigzag nanotubes. The reduction of planar hydrocarbon materials by lithium atoms has also been studied very systematically. We also illustrate the way in which noncovalent interactions can be used to optimize and fine-tune the properties of CNSs.